|CUOMO, CHRISTINA - Broad Institute Of Mit/harvard|
|BAKKEREN, GUUS - Agriculture And Agri-Food Canada|
|KHALIL, HALA - Agriculture And Agri-Food Canada|
|PANWAR, VINAY - Agriculture And Agri-Food Canada|
|JOLY, DAID - University Of Moncton|
|LINNING, ROB - Agriculture And Agri-Food Canada|
|SAKTHIKUMAR, SHARADHA - Broad Institute Of Mit/harvard|
|SONG, XIAO - Agriculture And Agri-Food Canada|
|GOLDBERG, JONATHAN - Broad Institute Of Mit/harvard|
|YOUNG, SARAH - Broad Institute Of Mit/harvard|
|ZENG, QIANDONG - Broad Institute Of Mit/harvard|
|MCCALLUM, BRENT - Agriculture And Agri-Food Canada|
|HULBERT, SCOTT - Washington State University|
Submitted to: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/24/2016
Publication Date: 12/2/2016
Citation: Cuomo, C.A., Bakkeren, G., Khalil, H., Panwar, V., Joly, D., Linning, R., Sakthikumar, S., Song, X., Goldberg, J., Young, S., Zeng, Q., Bruce, M.A., McCallum, B., Szabo, L.J., Hulbert, S., Chen, X., Fellers, J.P. 2016. Comparative analysis highlights variable genome content of wheat rusts and divergence of the mating loci. Genes, Genomes, Genetics. doi:10.1534/g3.116.032797.
Interpretive Summary: Three members of the Puccinia genus, P. triticina (Pt), P. striiformis f.sp. tritici (Pst), and P. graminis f.sp. tritici (Pgt), cause the most common and often most significant foliar diseases of wheat. While similar in biology and life cycle, each species is uniquely adapted and specialized. The genomes of Pt and Pst were sequenced and compared to that of Pgt to identify common and distinguishing gene content, to determine gene variation among wheat rust pathogens, other rust fungi and basidiomycetes, and to identify genes of significance for infection. Pt had the largest genome of the three, estimated at 135 Mb with expansion due to mobile elements and repeats encompassing 50.9% of contig bases; by comparison repeats occupy 31.5% for Pst and 36.5% for Pgt. We find all three genomes are highly heterozygous, with Pst (5.97 SNPs/kb) nearly twice the level detected in Pt (2.57 SNPs/kb) and that previously reported for Pgt. Of 1,358 predicted effectors in Pt, 784 were found expressed across diverse life cycle stages including the sexual stage. Comparison to related fungi highlighted the expansion of gene families involved in transcriptional regulation and nucleotide binding, protein modification, and carbohydrate enzyme degradation. Two allelic homeodomain, HD1 and HD2, pairs and three pheromone receptor (STE3) mating-type genes were identified in each dikaryotic Puccinia species. The HD proteins were active in a heterologous Ustilago maydis mating assay and host induced gene silencing of the HD and STE3 alleles reduced wheat host infection.
Technical Abstract: Wheat is grown around the world and has been plagued by three rust fungi for centuries. Leaf rust, stripe rust, and stem rust each cause significant damage and can adapt quickly to overcome resistance that is present in wheat cultivars. Using advanced DNA sequencing technology, the genomes of leaf and stripe rust were sequenced and compared to stem rust, and other related fungi. The three genomes vary in size, repetitive DNA elements, and the number of genes. Many genes are common to all three rusts, but many are unique to only one species and may reflect special adaptations to their hosts. The analysis of the genomic sequences may reveal weaknesses that can be exploited for improved control of the rust species that attack cereals.